Evaluation of commercial corn hybrids for agronomic traits and nitrogen use efficiency

O milho é uma das principais culturas agrícolas do mundo. Dos 15,8 milhões de hectares plantados com milho no Brasil, estima-se que 98% dessa área sejam cultivados com híbridos. O nitrogênio (N) é o nutriente consumido em maior quantidade pela planta de milho. Assim, os objetivos desse trabalho foram: i) avaliar híbridos comerciais de milho tropical para eficiência de utilização e remobilização de N em contratantes doses de N; ii) avaliar híbridos comerciais de milho tropicais para caracteres agronômicos em condições contrastantes de N e; iii) estudar a influência de caracteres agronômicos na produtividade de grãos e nas eficiências de utilização e remobilização de N em híbridos comerciais de milho tropical. Para realização desse trabalho foram utilizados 87 híbridos comerciais de milho, sendo avaliados na Estação Experimental de Coimbra, Coimbra-MG, na safra 2015/2016. Foram realizados dois experimentos, um em baixa dose (18 kg ha -1 de N), e outro em alta dose de N (198 kg ha -1 de N). Cada experimento foi realizado em delineamento de blocos casualizados com três repetições. Cada parcela foi constituída de duas linhas de milho com quatro metros de comprimento, espaçadas em 0,80 m. Foram avaliados os seguintes caracteres: área foliar, altura de planta, diâmetro de colmo (DC), teor de clorofila (SPAD), comprimento de entrenó, número de fileiras, comprimento de espiga, profundidade de grão, massa hectolítrico (PHE), massa de 1000 grãos, biomassa no florescimento, colheita e total, concentração de N no florescimento, na colheita e nos grãos, conteúdo de N da biomassa no florescimento, colheita, grãos e total, absorção pós-antese (NPA), N remobilizado, eficiência de remobilização, eficiência na utilização de N (EUtN), índice de colheita de N (ICN) e produtividade de grãos. Comprovou-se variabilidade genética entre os híbridos comerciais de milho para caracteres relacionados à utilização de N. Houve efeito significativo para EUtN em ambos ambientes. Os híbridos mais produtivos em alto N foram BM709PRO2, P3456H e BM3063PRO2. Os híbridos mais produtivos em baixo N foram BM709PRO2, RB9004PRO e BM3061. Em geral, a diferença de dose de N no solo influenciou o desempenho dos caracteres, diminuindo as médias, mas, para PHE, EUtN, NPA e ICN observou-se maiores médias no ambiente de baixo N. Os caracteres DC e SPAD, podem ser considerados na seleção indireta de híbridos de milho mais eficientes na utilização e na remobilização de nitrogênio.Corn is a major crop in the world. Of the 15.8 million hectares of maize in Brazil, it is estimated that 98% of this area is cultivated with hybrids. Nitrogen (N) is the nutrient consumed in greater quantities by the corn plant. The objectives of this study were: i) to evaluate tropical maize hybrids for commercial use efficiency and remobilization of N at contrasting doses of N; ii) evaluate commercial hybrids of tropical maize for agronomic traits in contrasting conditions of N and; iii) to study the influence of agronomic traits in grain yield and efficiencies and remobilization of N in commercial hybrids of tropical maize. To carry out this work were used 87 commercial corn hybrids were evaluated at the Experimental Station of Coimbra, Coimbra, MG, at harvest 2015/2016. Two experiments were conducted, one in low dose (18 kg N ha -1 ) , and one high dose of N (198 kg N ha -1 ) . Each experiment was conducted in a randomized block design with three replications. Each plot consisted of two rows of corn four meters long, spaced at 0.80 m. We evaluated the following characters: leaf area, plant height, stem diameter (SD), ear leaf chlorophyll concentration (SPAD), length of internodes, kernel rows, ear length, depth of grain, hectoliter weight, one thousand kernel weight, biomass in flowering, harvest and total, N concentration at flowering, harvesting and grain, N content of the biomass at flowering, harvest, grain and total, post-silking absorption, N remobilized, remobilization efficiency, N utilization efficiency (NUtE), N harvest index (NHI) and grain yield. Verified to be genetic variability among commercial corn hybrids for traits related to the use of N. There was a significant effect for NUtE in both environments. The most productive hybrids in high N were BM709PRO2, P3456H and BM3063PRO2. The most productive hybrids in low N were BM709PRO2, RB9004PRO and BM3061. In general, N rate influence the performance of the characters, reducing the average, but for PHE, NUtE, NPA and NHI observed higher average at low dose. The SD and SPAD characters can be considered in the indirect selection of more efficient maize hybrids in use and nitrogen remobilization.Conselho Nacional de Desenvolvimento Científico e Tecnológic

Combinando conjunto de dados GBS para o estudo de GWAS e GWS para características de arquitetura de raiz de milho

Maize has a sophisticated and complex root architecture that is important for plant anchorage and uptake of nutrients and water. Tools such as genome-wide association (GWAS) and genome-wide selection (GWS) can help the breeders to make decisions about which genotypes should advance in their breeding programs. In this work, we combined two data sets with different genetic backgrounds to perform a GWAS and GWS analysis in different scenarios. Our hypothesis was that combining the genomic data from different backgrounds may increase the power of detecting significant polymorphisms associated with maize seedling root traits and increase prediction accuracy. We used 679 inbred lines, 377 from Ames Panel and 302 from BGEM Panel. The root seedlings phenotype was obtained via image software from plants 14 days old grown in paper rolls in a growth chamber. We evaluated five root traits: depth, lateral root length, primary root length, total number of roots and total root length. Our study is singular by combining two SNP (Single Nucleotide Polymorphism) data sets with different genetic backgrounds to access the prediction accuracy within, across and combining the populations or subpopulations on root traits in maize. After quality control, 232,460 SNPs were used in further analysis. Population structure analysis revealed four groups that were used to build the scenarios for GWS and to control false positives in GWAS analysis. GWAS showed a total of 13 SNPs above the significance threshold. Those SNPs led to 10 candidate genes. At GWS, the combined scenario had the highest accuracy (0.66) across all traits, followed by non- stiff-stalk combined (0.63) and stiff-stalk combined (0.56). The scenarios that we calculated the prediction accuracy across panels showed the low accuracies (all were lower than 0.25). As seen in this study, combine results across studies is useful, even with different backgrounds, to improve the GWS accuracy and detect significant polymorphisms associated with maize seedling root traits and allocate the individuals from the combined data set in groups by using population structure analysis is advantageous. The genes found can be further studied to help understand the genetic basis of root development and improve the root architecture. Keywords: Zea mays. Genomic selection. Association Mapping. Population structureO milho possui uma arquitetura de raiz sofisticada e complexa que é importante para a ancoragem das plantas e a absorção de nutrientes e água. Ferramentas como a associação genômica ampla (GWAS) e a seleção genômica ampla (GWS) podem ajudar os melhoristas a tomar decisões sobre quais genótipos devem avançar em seus programas de melhoramento. Neste trabalho, combinamos dois conjuntos de dados de duas populações com diferentes ascendências para executar análise de GWAS e GWS em diferentes cenários. Nossa hipótese foi que a combinação de dados genômicos, mesmo com diferentes ascendências, pode aumentar o poder de detectar polimorfismos significativos associados às características radiculares de milho e aumentar a acurácia da predição. Nós utilizamos 679 linhagens de milho, 377 da população Ames e 302 da população BGEM. Os fenótipos de plântulas radiculares foram obtidos via software de imagem com 14 dias de idade cultivadas em rolos de papel em uma câmara de crescimento. Foram avaliados cinco caracteres de raiz: profundidade, comprimento de raízes laterais, comprimento da raiz principal, número total de raízes e comprimento total de raízes. Nosso estudo é singular por combinar dois conjuntos de dados SNP (Single Nucleotide Polymorphism) com diferentes ascendências para acessar a acurácia de predição entre, através e combinando as populações e subpopulações de caracteres de raiz de milho. Após controle de qualidade dos dados genotípicos, 232.460 SNPs foram utilizados nas análises. Análise de estrutura de população revelou total de quatro subpopulações, das quais foram formados os cenários para GWS e controle de falsos positivos na análise de GWAS. Na GWAS, um total de 13 SNPs acima do limite significativo foi detectado. Esses SNPs levaram a 10 genes candidatos. Na GWS, o cenário combinado teve a maior precisão (0,66) em todas as características, seguido pelo NSSS combinado (0,63) e SSS combinado (0,56). Os cenários em que calculamos a acurácia de predição entre populações apresentaram as menores precisões (todas com menos de 0,25). Como visto neste trabalho, combinar resultados entre estudos é útil para melhorar a precisão da GWS e detectar polimorfismos significativos associados às características radiculares de milho, mesmo com diferentes ascendências e separar o conjunto de dados combinado em grupos através de análise de estrutura de população é eficaz. Os genes encontrados podem ser mais estudados para ajudar a entender a base genética do desenvolvimento radicular e aprimorar a arquitetura. Palavras-chave: Zea mays. Seleção genômica. Mapa de associação. Estrutura de população

Combining data sets for maize root seedling traits increases the power of GWAS and genomic prediction accuracies

The identification of genomic regions associated with root traits and the genomic prediction of untested genotypes can increase the rate of genetic gain in maize breeding programs targeting roots traits. Here, we combined two maize association panels with different genetic backgrounds to identify SNPs significantly associated with root traits and through of genome-wide association study (GWAS) and to assess the potential of genomic prediction these traits in maize. For this, we evaluated 377 lines from the Ames and 302 from the BGEM (Backcrossed Germplasm Enhancement of Maize) panels in a Combined panel of 679 lines. The lines were genotyped with 232,460 SNPs, and four root traits were collected from 14-day old seedlings. We identified 30 SNPs significantly associated with root traits in the Combined panel, whereas only two and six SNPs were detected in the Ames and BGEM panels, respectively. Those 38 SNPs were in linkage disequilibrium with 35 candidate genes. In addition, we found higher prediction accuracy in the Combined panel than in the Ames or BGEM panels. We concluded that combining association panels appear to be a useful strategy to identify candidate genes associated with root traits in maize and improve the efficiency of the genomic prediction.This is a pre-copyedited, author-produced version of an article accepted for publication in Journal of Experimental Botany following peer review. The version of record: Tonello Zuffo, Leandro, Rodrigo Oliveira DeLima, and Thomas Lübberstedt. "Combining data sets for maize root seedling traits increases the power of GWAS and genomic prediction accuracies." Journal of Experimental Botany (2022) is available online at DOI: 10.1093/jxb/erac236. Copyright 2022 The Author(s). Posted with permission

Usefulness of Adapted Exotic Maize Lines Developed By Doubled Haploid and Single Seed Descent Methods

Adapted exotic maize (Zea mays L.) germplasm, such as BS39, provides a unique opportunity for broadening the genetic base of U.S. Corn Belt germplasm. In vivo doubled haploid (DH) technology has been used to efficiently exploit exotic germplasm. It can help to purge deleterious recessive alleles. The objectives of this study were to determine the usefulness of BS39-derived inbred lines using both SSD and DH methods, to determine the impact of spontaneous as compared to artificial haploid genome doubling on genetic variance among BS39-derived DH lines, and to identify SNP markers associated with agronomic traits among BS39 inbreds monitored at testcross level. We developed two sets of inbred lines directly from BS39 by DH and SSD methods, named BS39_DH and BS39_SSD. Additionally, two sets were derived from a cross between BS39 and A427 (SHGD donor) by DH and SSD methods, named BS39×A427_DH and BS39×A427_SSD, respectively. Grain yield, moisture, plant height, ear height, stalk lodging, and root lodging were measured to estimate genetic parameters. For genome-wide association (GWAS) analysis, inbred lines were genotyped using Genotype-by-Sequencing (GBS) and Diversity Array Technology Sequencing (DArTSeq). Some BS39-derived inbred lines performed better than elite germplasm inbreds and all sets showed significant genetic variance. The presence of spontaneous haploid genome doubling genes did not affect performance of inbred lines. Five SNPs were significant and three of them located within genes related to plant development or abiotic stresses. These results demonstrate the potential of BS39 to add novel alleles to temperate elite germplasm.This is a preprint made available through Research Square at doi:10.21203/rs.3.rs-799789/v1. This work is licensed under a CC BY 4.0 License

Major locus for spontaneous haploid genome doubling detected by a case–control GWAS in exotic maize germplasm

Temperate maize (Zea mays L.) breeding programs often rely on limited genetic diversity, which can be expanded by incorporating exotic germplasm. The aims of this study were to perform characterization of inbred lines derived from the tropical BS39 population using different breeding methods, to identify genomic regions showing segregation distortion in lines derived by the DH process using spontaneous haploid genome doubling (SHGD), and use case-control association mapping to identify loci controlling SHGD. Four different sets were used: BS39_DH and BS39_SSD were derived from the BS39 population by DH and single-seed descendent (SSD) methods, and BS39×A427_DH and BS39×A427_SSD from the cross between BS39 and A427. A total of 663 inbred lines were genotyped. The analyses of gene diversity and genetic differentiation for the DH sets provided evidence of the presence of a SHGD locus near the centromere of chromosome 5. The case-control GWAS for the DH set also pinpointed this locus. Haplotype sharing analysis showed almost 100% exclusive contribution of the A427 genome in the same region on chromosome 5 of BS39×A427_DH, presumably due to an allele in this region affecting SHGD. This locus enables DH line production in exotic populations without colchicine or other artificial haploid genome doubling.This is a manuscript of an article published as Verzegnazzi, A.L., dos Santos, I.G., Krause, M.D. et al. Major locus for spontaneous haploid genome doubling detected by a case–control GWAS in exotic maize germplasm. Theor Appl Genet (2021). doi: 10.1007/s00122-021-03780-8. Posted with permission.</p